General Overview

IMAP stands for Integrated Microbiome Analysis Pipelines, developed independenly as standalone GitHub repositories. When used sequentially, all IMAP parts provide a systematic microbiome data analysis beyond the traditional methods.





Repo-specific RMD Chunks

Chunk 01

Chunk 02

Chunk 03




References

[1]
Buza, T. M., Tonui, T., Stomeo, F., Tiambo, C., Katani, R., Schilling, M., … Kapur, V. (2019). iMAP: An integrated bioinformatics and visualization pipeline for microbiome data analysis. BMC Bioinformatics, 20. https://doi.org/10.1186/S12859-019-2965-4



Appendix

Project main tree

.
├── LICENSE
├── README.md
├── config
│   ├── config.yml
│   ├── pbs
│   ├── samples.tsv
│   ├── slurm
│   └── units.tsv
├── dags
├── data
├── images
│   ├── bkgd.png
│   ├── cicd.png
│   ├── imap.png
│   └── smkreport
├── index.Rmd
├── library
│   ├── apa.csl
│   ├── imap.bib
│   └── references.bib
├── report
│   └── report.html
├── report.html
├── requirements.txt
├── resources
├── results
│   └── project_tree.txt
├── styles.css
├── templates
└── workflow
    ├── Snakefile
    ├── envs
    ├── rules
    ├── schemas
    └── scripts

18 directories, 18 files

Screenshot of interactive snakemake report

The interactive snakemake HTML report can be viewed by opening the report.html using any compatible browser. You will be able to explore the workflow and the associated statistics. You can close the left bar to get a more expansive display view.

Troubleshooting of FAQs

  1. Question
    • Answer
  2. Question
    • Answer